Is it possible to use some tool in Galaxy to convert BED file to Bam/ sam
file. In other word do we have Bed tools or other option in Galaxy
Thanks
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Hello,
It is possible to go from SAM/BAM to BED, but not the reverse. SAM/BAM
files contain the actual sequence data associated with the original
aligned read. BED files only have the reference genome location of the
alignment (no read "sequence").
It is possible to extract genomic sequence
Thanks Jen,
My problem is I have ChIP-seq data where I have one Bed
file with coordinates-
chr1 724027 724226 61PDWAAXX100706:4:19:6952:18071 -
Then there is wig file.? Is it possible that thsi data can be analyzed in
Galaxy/ Cistrome. I tried to use Cistrome which gav eme error
Hello,
The format of the BED file may be a problem. To be in BED format, an
additional field is required for the "score" attribute. This would be
column 5, moving the strand out to column 6.
To do this:
1 - use "Text Manipulation->Add column" with the value "0"
note: "0" often is used to rep
This is what I followed:
1. Upload the Bed file (60) > Text manipulation Add column –add this
value 0; iterate –no will give file 73
2. 73 > Txt manipulation – cut > c1,c2,c3,c4,c6,c5 and delimited by
tab- give file 74
3. 74> pencil icon> change data type – tabular – file
Now when I run the same files in the main Galaxy server it gave me following
errors, Do you have any suggestion how these same files will be working ion
Develop server but not on main server using same steps.
INFO @ Tue, 04 Oct 2011 14:56:21: # ARGUMENTS LIST: # name = MACS_in_Galaxy
# format = BE
Hello,
The last line of the report you sent suggests that the file has format
problems. I read through your other email and noticed that a few steps
were inserted, perhaps because they were needed. However, the line noted
here is not in BED format:
On 10/4/11 12:06 PM, shamsher jagat wrote:
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